Vatican experts soon will make a public announcement of their discovery, Catholic World News said.
"The tomb that we discovered is the one that the popes and the Emperor Theodosius [A.D. 379- 395] saved and presented to the whole world as being the tomb of the apostle," Filippi said.
The excavation was conducted after the administrator of St. Paul's basilica, Archbishop Francesco Gioia, received inquiries about the location of St. Paul's tomb from thousands of pilgrims visiting during the Jubilee Year of 2000.
An initial survey of the basilica enabled archeologists to reconstruct the 4th century building's original shape.
The Vatican team found the sarcophagus during a second excavation under the basilica's main altar.
Under the altar, a marble plaque is visible, dating to the 4th century, bearing the inscription "Apostle Paul, martyr."
Surprisingly, said Filippi, "nobody ever thought to look behind that plaque," where the Vatican team found the sarcophagus.
Filippi said the tomb should not be opened merely to satisfy curiosity as to whether Paul's remains still are there.
He has no doubt, however, Paul was buried on the site, "because this basilica was the object of pilgrimages by emperors; people from all around the world came to venerate him, having faith that he was present in this basilica."
Filippi said church officials must now decide whether to order further excavation to make the sarcophagus more visible.
The Bible does not state how Paul died. Many scholars believe he was beheaded in Rome in about the A.D. mid-60s during the reign of Roman Emperor Nero.